ROS1 mutations promote an immunosuppressive tumor microenvironment via MYC to confer immune evasion in head and neck cancer

<b>Aim:</b> Immune checkpoint inhibitors (ICIs) have transformed cancer therapy; however, their efficacy in head and neck cancer (HNC) remains limited, with only a minority of patients achieving durable responses. Understanding the molecular mechanisms underlying ICI resistance in HNC is therefore crucial. <b>Methods:</b> We conducted an integrative analysis of genomic, transcriptomic, and clinical data from 139 ICI-treated HNC patients (MSKCC cohort) and 502 treatment-naïve HNC cases (TCGA cohort). <i>ROS1</i> mutation status, tumor mutational burden (TMB), neoantigen load, immune cell infiltration (via CIBERSORT), and immune-related gene expression were evaluated. Gene set enrichment analysis (GSEA) was performed to identify dysregulated pathways. Survival outcomes were assessed using Kaplan-Meier analysis and Cox regression, with statistical significance defined as <i>P</i> < 0.05. <b>Results:</b> Patients harboring <i>ROS1</i> mutations exhibited significantly poorer outcomes following ICI therapy, with shorter median overall survival [OS: 5.0 <i>vs.</i> 11.0 months, hazard ratio (HR) = 3.22, 95%CI: 1.26-8.19, <i>P</i> = 0.011] compared to <i>ROS1</i> wild-type counterparts. Multivariate analysis confirmed <i>ROS1</i> mutation as an independent predictor of poor OS in ICI-treated patients (HR = 4.78, 95%CI: 1.70-13.43, <i>P</i> = 0.003). In contrast, <i>ROS1</i> mutations showed no prognostic significance in the treatment-naïve TCGA-HNC cohort (<i>P</i> = 0.26), confirming their role as a predictive (not prognostic) biomarker for ICI response. Interestingly, despite exhibiting higher TMB and neoantigen levels, <i>ROS1</i>-mutant patients showed inferior survival, underscoring the context-dependent limitations of TMB as a predictive biomarker. Mechanistically, <i>ROS1</i>-mutant tumors displayed an immunosuppressive tumor microenvironment characterized by diminished CD8⁺ T cell infiltration, attenuated interferon-γ signaling, and downregulation of immune-related genes (<i>CXCL9</i>, <i>CXCL10</i>, <i>IFNG</i>, <i>PD-L1</i>). GSEA revealed enrichment of <i>MYC</i> pathway activity in <i>ROS1</i>-mutant tumors, which suppressed antigen presentation and T cell activation pathways. <b>Conclusion:</b> <i>ROS1</i> mutations drive ICI resistance in HNC by promoting an immunosuppressive TME via <i>MYC</i>-mediated transcriptional reprogramming, impairing antigen presentation and T cell function. Incorporating <i>ROS1</i> status into biomarker panels may improve patient stratification and guide combinatorial therapies targeting both immune evasion and oncogenic pathways.